While English has no consistent rule regarding the two prefixes, it’s fair to say that the French en- has bested the Latin in- most of the time.
Usually, when preceding a root form beginning with -b-, -m-, or -p-, the en- and in- prefixes have evolved into em- and im-: embalm, embank, embody, embroider, empower, imbue, immemorial, immense, immolate, impale, impoverish, etc. With other root forms, en- and in- usually prevail: encumber, ensnare, enshrine, entitle, entrap, inflame, inquire, inure, etc.
Some words have developed with both prefixes, such as ensure and insure (see ensure or insure), or have developed varying prefixes depending on the form, such as encrust and incrustation. Use a reliable dictionary when in doubt of the correct prefix.